Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (SAMPLE_PAIRED_END_1_1)'

Caused by:
  Process `NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (SAMPLE_PAIRED_END_1_1)` terminated with an error exit status (1)


Command executed:

  INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb$//'`
  
  bwa-mem2 \
      mem \
       \
      -t 2 \
      $INDEX \
      Bpacificus-ATCC10987-rep1-sWGS-MiSeqi100-241111_S1_L001_R1_001.fastq.gz Bpacificus-ATCC10987-rep1-sWGS-MiSeqi100-241111_S1_L001_R2_001.fastq.gz \
      | samtools sort  -@ 2  -o SAMPLE_PAIRED_END_1_1.bam -
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM":
      bwamem2: $(echo $(bwa-mem2 version 2>&1) | sed 's/.* //')
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
  Looking to launch executable "/opt/conda/bin/bwa-mem2.sse42", simd = .sse42
  Launching executable "/opt/conda/bin/bwa-mem2.sse42"
  -----------------------------
  Executing in SSE4.2 mode!!
  -----------------------------
  * SA compression enabled with xfactor: 8
  * Ref file: ./genome.fa
  * Entering FMI_search
  ERROR! Unable to open the file: ./genome.fa.bwt.2bit.64
  [W::hts_set_opt] Cannot change block size for this format
  samtools sort: failed to read header from "-"

Work dir:
  /Users/agrimabhatt/seqinspector/work/d0/4c595c9b0edfe8a64a1469cacb13c0

Container:
  community.wave.seqera.io/library/bwa-mem2_htslib_samtools:e1f420694f8e42bd

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`